External Email - Use Caution

Hi Bruce,

I managed to overcome said error but now during example 2 another error pops up.

Skol-MacBook-Pro:~ kskol$ export SUBJECTS_DIR=<path to subject directory>

-bash: syntax error near unexpected token `newline'

Thanks,

Konstantina

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: 09 July 2018 17:17 To: Freesurfer support list Subject: Re: [Freesurfer] niiWrite(): error opening file tmp.nii

Hi Konstantina

do you have write access to the partition you are putting the subjects_dir on? And can you please send us the full command line, screen output and recon-all.log?

cheers Bruce

On Mon, 9 Jul 2018, Konstantina Skolariki wrote:

    External Email - Use Caution

Hi FreeSurfer Developers, I have downloaded freesurfer on my mac and after "setup & configuration” I tried to perform example 1 from "test your FreeSurfer Installation”. However when I type the command, this error message shows up:

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to tmp.nii... niiWrite(): error opening file tmp.nii ERROR: failure writing tmp.nii

Thanks, Konstantina

External Email - Use Caution

Hi Bruce,

This is my full command line! I just started using this and I am not really sure what you mean by recon-all.log.

Skolarikis-MacBook-Pro:~ kskol$ export FREESURFER_HOME=/Applications/freesurfer Skolarikis-MacBook-Pro:~ kskol$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Skolarikis-MacBook-Pro:~ kskol$ export SUBJECTS_DIR 'pwd' Skolarikis-MacBook-Pro:~ kskol$ echo $SUBJECTS_DIR/ /Applications/freesurfer/subjects/ Skolarikis-MacBook-Pro:~ kskol$ cp $FREESURFER_HOME/subjects/sample-001.mgz . Skolarikis-MacBook-Pro:~ kskol$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... Skolarikis-MacBook-Pro:~ kskol$ export SUBJECTS_DIR=/Applications/freesurfer Skolarikis-MacBook-Pro:~ kskol$ recon-all -i sample-001.nii.gz -s bert -all mkdir: /Applications/freesurfer/bert: Permission denied mkdir: /Applications/freesurfer/bert/scripts: Permission denied mkdir: /Applications/freesurfer/bert/scripts: Permission denied cp: /Applications/freesurfer/bert/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/bert/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/bert/scripts/patchdir.txt: No such file or directory. Skolarikis-MacBook-Pro:~ kskol$

Thanks, Konstantina On 9 Jul 2018, at 15:33, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Konstantina

can you include the full command line, screen output and recon-all.log in the type of email? Otherwise it will be difficult for us to help thanks Bruce

On Mon, 9 Jul 2018, Konstantina Skolariki wrote:

External Email - Use Caution Hi Bruce, I managed to overcome said error but now during example 2 another error pops up. Skol-MacBook-Pro:~ kskol$ export SUBJECTS_DIR=<path to subject directory> -bash: syntax error near unexpected token `newline' Thanks, Konstantina ____________________________________________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: 09 July 2018 17:17 To: Freesurfer support list Subject: Re: [Freesurfer] niiWrite(): error opening file tmp.nii Hi Konstantina do you have write access to the partition you are putting the subjects_dir on? And can you please send us the full command line, screen output and recon-all.log? cheers Bruce On Mon, 9 Jul 2018, Konstantina Skolariki wrote:

    External Email - Use Caution

Hi FreeSurfer Developers, I have downloaded freesurfer on my mac and after "setup & configuration” I tried to perform

example

1 from "test your FreeSurfer Installation”. However when I type the command, this error message shows up:

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to tmp.nii... niiWrite(): error opening file tmp.nii ERROR: failure writing tmp.nii

Thanks, Konstantina

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